[gmx-users] NMA proctocol

[Yao Yao]

Hi Gmxers,


For Normal Mode Analysis (NMA), even I did run several rounds to aim for machine precision, with smaller emtol stepwise,
it still did not converge to 0.001 and the Fmax is about 0.5 or so. It is just lysozyme in 200 water molecules.

I wonder if there is a systematic way to guarantee the convergence, or I have to await luck to come.
Because I am pretty sure if I continue with NMA, I will get translational and rotational modes in final eigenfrequencies.

thanks,

Yao   



On 11/16/12 3:43 PM, Yao Yao wrote:
> Hi Gmxers,
>
> I am doing a protein NMA with the mdp file like,
>
> ===========================================
>
>
> define          = -DEFLEXIBLE
> constraints     = none
> integrator      = nm ;
> emtol           = 0.00001
> emstep          = 0.1
> nsteps          = 4000  ; Maximum number of (minimization) steps to perform
>
> ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
> nstlist         = 0 ; Frequency to update the neighbor list and long range forces
> ns_type         = simple        ; Method to determine neighbor list (simple, grid)
> ;vdwtype 
        = switch
> vdwtype         = cut-off
> rlist           = 0.0   ; Cut-off for making neighbor list (short range forces)
> ;coulombtype    = PME-switch    ; Treatment of long range electrostatic interactions
> coulombtype     = cut-off
> ;rcoulomb       = 1.2   ; Short-range electrostatic cut-off
> rcoulomb        = 0.0
> ;rvdw           = 1.2   ; Short-range Van der Waals cut-off
> rvdw            = 0.0
> pme_order       = 4
> fourierspacing  = 0.12
> fourier_nx  = 0
> fourier_ny  = 0
> fourier_nz  = 0
> optimize_fft    = yes
> pbc             = no
>
 =====================================================
>   However, it shows
>
>
> "Fatal error:
> Constraints present with Normal Mode Analysis, this combination is not supported"
>
> Since I put "Constaints" none, I really do not get it. Can someone help me?
>

The problem is a typo.  You've set "-DEFLEXIBLE" instead of "-DFLEXIBLE" so 
rather than having flexible water as intended, you've got rigid water via the 
SETTLE algorithm, and constraints are still present.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================